2q2u

Structure of Chlorella virus DNA ligase-product DNA complex

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorella virus DNA ligase

Paramecium bursaria Chlorella virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPT)-3' × 1 5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAPA)-3' × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPT)-3' × 1 5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAPA)-3' × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPT)-3' × 1 5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAPA)-3' × 1 water × 2	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPT)-3' × 1 5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAPA)-3' × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O41026_PBCV1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 22–319； UniProt 1–298 Author chain B； PDBConstruct 22–319； UniProt 1–298 Author chain C； PDBConstruct 22–319； UniProt 1–298 Author chain D； PDBConstruct 22–319； UniProt 1–298

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2q2u
Deposition date deposition_date	2007-05-29
Structure title title	Structure of Chlorella virus DNA ligase-product DNA complex
Keywords keywords	LIGASE, PRODUCT-COMPLEX, PROTEIN-DNA COMPLEX, LIGASE-DNA COMPLEX; LIGASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2q2u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q2u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2q2u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.80 Å
Rg (electron density)	22.02 Å
Total Rg	22.78 Å
Atom count	3217
Residues	334
Excluded volume	54934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q2u__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q2u__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2q2u__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2q2u__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAP*T)-3'
Molecular weight formula_weight	6494.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,I,K
Atom count atom_count	12924

TTCCGATAGTGGGGTCGCAAT

Entity 2 Entity 2 polymer

Description description	5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAP*A)-3'
Molecular weight formula_weight	6422.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	F,H,J,L

ATTGCGACCCCACTATCGGAA

Entity 3 Entity 3 polymer

Description description	Chlorella virus DNA ligase
Molecular weight formula_weight	36833.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

MGHHHHHHHHHHSSGHIEGRHMAITKPLLAATLENIEDVQFPCLATPKIDGIRSVKQTQMLSRTFKPIRNSVMNRLLTELLPEGSDGEISIEGATFQDTTSAVMTGHKMYNAKFSYYWFDYVTDDPLKKYIDRVEDMKNYITVHPHILEHAQVKIIPLIPVEINNITELLQYERDVLSKGFEGVMIRKPDGKYKFGRSTLKEGILLKMKQFKDAEATIISMTALFKNTNTKTKDNFGYSKRSTHKSGKVEEDVMGSIEVDYDGVVFSIGTGFDADQRRDFWQNKESYIGKMVKFKYFEMGSKDCPRFPVFIGIRHEEDR

Source Source

Source organism organism	Paramecium bursaria Chlorella virus 1
NCBI taxonomy ID ncbi_taxonomy_id	10506
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2q2ua1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d2q2ua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.1 — ATP-dependent DNA ligase catalytic domain

Domain ID domain_id	d2q2ub1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d2q2ub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.1 — ATP-dependent DNA ligase catalytic domain

Domain ID domain_id	d2q2uc1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d2q2uc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.1 — ATP-dependent DNA ligase catalytic domain

Domain ID domain_id	d2q2ud1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain

Domain ID domain_id	d2q2ud2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.1 — ATP-dependent DNA ligase catalytic domain

CATH v4.4 (12 domains)

Domain ID domain_id	2q2uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2q2uA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	2q2uA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2q2uB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2q2uB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	2q2uB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2q2uC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2q2uC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	2q2uC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2q2uD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2q2uD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	2q2uD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	66.475 Å
Unit-cell length b length_b	92.895 Å
Unit-cell length c length_c	89.633 Å
Unit-cell angle α angle_alpha	70.32 °
Unit-cell angle β angle_beta	78.45 °
Unit-cell angle γ angle_gamma	89.87 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	24.880 Å
R factor r_factor	—
R_work r_work	0.2490
R_free r_free	0.2830

Structure of Chlorella virus DNA ligase-product DNA complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorella virus DNA ligase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2q2u__assembly_1__model_1

2q2u__assembly_1__model_1 | I(q)

2q2u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of Chlorella virus DNA ligase-product DNA complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorella virus DNA ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2q2u__assembly_1__model_1

2q2u__assembly_1__model_1 | I(q)

2q2u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)